Raytraced transparency not showing other transparent materials beneath?
You should check the Traceable property on the Eye_transparent material. This allows the material to be evaluated during raytracing calculations and will therefore let the specular highlight on the Eye_transparent geometry be seen through the raytraced glass.

This isn't strictly related to your original question, but I'd also recommend enabling mirror raytracing on your lens material to increase their realism. I recommend setting reflectivity to 1, fresnel to 3.5 and blend to 1.15. Fresnel reflectivity is really important to capture accurately for a realistic render, particularly for glass and water materials. I also think that your skin material could benefit from lowering the subsurface scattering radius a little bit. This is just my two cents and of course for a glass material to look really good it has to have an environment to reflect.